Command Agreement Alternate Universe
by gawilliams
Summary: What if Janeway had a different command arrangement in mind at the end of Caretaker?


Command Agreement Alternate Universe

Disclaimer: I don't own or have a share in the profits from these characters or the franchise. No copyright infringement is intended.

"It is logical," Tuvok admitted as he looked carefully at his Captain.

Kathryn sighed in relief. She knew what she was proposing was something that she should not be contemplating, but the circumstances Voyager now found herself in were beyond anything that anyone at Starfleet could have dreamed of. It was their best chance of getting home.

"But will he agree to it?" she asked. For all she had read and reread Captain Chakotay's intelligence files, Tuvok had served with the man and knew him far better.

Tuvok raised a brow. "Captain Chakotay is a very experienced Captain and an honorable man," he pointed out. "I believe that he will be resistant to this proposed course of action, but he will listen and consider it carefully before making any kind of decision. It is imperative that you be completely forthright with him, though, Captain. He will not react well to anything less than the full truth."

Kathryn nodded. "Please escort him here, Tuvok and then leave us to our discussion," she ordered.

"Understood, Captain," Tuvok replied as he stood and left the Ready Room.

Fifteen minutes later she was going over the latest Engineering reports from Lieutenant Carey and not liking the picture they were painting. The ship was, for lack of anything better to say, a shambles. The main engines were holding together, but barely. Weapons were online, but fluctuating, as with the shields. They had had to shut down the replicators, with the exception of the engineering replicators because of the power drain. The one good point was that life support was functioning at 100. The chime rang.

"Come," she said as she took a calming breath and put down the PADD. She watched as Captain Chakotay walked into the Ready Room and stood at attention before her.

"You wished to see me, Captain," Chakotay stated. Not the expected reply of an officer, but then he was not about to follow protocol and hint that he had respect for Starfleet.

"We need to have a serious discussion, Captain Chakotay," she said bluntly as she stood and walked over to the couch under the view ports.

"Considering the extensive maintenance and repairs I saw as I was escorted here, I'm not surprised," he acknowledged as he took a seat and accepted a glass of cold water.

Kathryn passed him the engineering report, and while he skimmed it she gave him an overall summary of the tactical and strategic picture that Voyager was facing. She was encouraged when he asked a few pointed questions that demonstrated he had a very quick grasp of the problems. His service record was filled with commendations and notations of his quick mind and sharp attention to detail.

"I have a proposal for you," she said when he said he'd heard and read enough to know what was happening.

"I'm listening," he said with a sigh. He was not thrilled with the situation, but he was honest enough with himself to admit she had been completely honest and above board from the moment they had met. She deserved the courtesy of being listened to.

"I don't have enough crew left to man and operate Voyager, and you don't have a ship after you sacrificed yours on our behalf," she stated the obvious. "I propose that we join our crews and utilize our skills to try to get home. I won't lie and say we can get there in a few years, but I hope we don't take the 75 that we are realistically facing."

"Why would my crew want to return to the Federation?" Chakotay asked.

Kathryn was forced to admit that that was a legitimate question. His crew, and himself, were facing criminal charges. If the situation in the Federation had not changed by the time they returned, they would be arrested. She did have one ace up her sleeve, though.

"I can't guarantee that you won't face charges, Captain, but you should know that the person who sent me on this mission was the President, and it is on record that the President has never been in favor of deeming the Maquis terrorists and criminals," she told him. "My views about the treaty with Cardassia and also about how the Maquis have been portrayed are also equally on record. If they had wanted someone who was serious about prosecuting the Maquis, they would not have sent me."

He nodded in agreement with that. He had heard of her over the years and her vocal opposition to the Treaty and the DMZ had bordered on insubordination. She had been just as heedless of the consequences when she had spoken about the Maquis.

"I can see the advantage of joining together, though I would reserve judgment on returning to the Federation," he conceded hesitantly.

She was pleased that he was at least willing to consider returning.

"Can we at least agree that this region of space is too contentious for us to stay in and that even if we decided to settle down somewhere, it needs to be well away from Kazon inhabited space?" she asked.

"That I can agree with," he admitted.

"Then could we take that one step further and agree that since we have to move on, we can move in the direction of Federation space and long term decisions can be made based on what we find beyond this region and how the crew develops as a single unit?" she asked.

"That would be acceptable," he said with a smile. He was pleasantly surprised at how in sync he was with her thinking. She was intelligent and willing to concede on detail to get the broader whole accomplished. In this case, the broader whole was uniting the two crews, which he had already decided was necessary. The long term destination was a detail best left for another day. He was pretty certain that heading for the Federation was something that even his people would decide to do once things had evened out on the ship and they felt like part of a genuine team. That, though, was not today and should be deferred until a better time.

"Then I propose that you take command of Voyager with your Starfleet commission of Captain returned," she told him. The clear shock on his face was proof that he had not even considered that option. "I would become First Officer."

"I don't want command of Voyager," Chakotay stated directly.

Kathryn looked at him pointedly so that he would see that she was serious. "I don't want to turn over my command, either, but this is not an ordinary situation, Captain," she explained. "No matter where we go in the Quadrant, we are alone and explorers. There is no backup and no assistance unless we negotiate and trade for it. You have an exemplary record of command in Starfleet, and almost all of it on long range missions well out of contact with Starfleet. You also learned to command a ship alone in dire circumstances when you commanded your ship in the Maquis. Having been a professor of Advanced Tactics at the Command School, you have a grasp of tactical and strategic situations and thinking that I don't have. I only received my present rank three months ago and this is my first command. I don't have nearly the experience or skills to command a ship under these circumstances when someone like you is here. Face it, Captain, you're the best chance these crews have to stay alive."

Chakotay looked away. He was not sure he liked this. First he wanted to make sure his crew was well cared for and safe. Then he wanted to make sure that whatever happened, Janeway's crew was able to get home if all were agreed. This was her ship and command, though. He did not feel right at all about accepting the command and making her a subordinate officer. Would the Starfleet crew accept such a situation? Would Janeway be able to exercise any kind of command authority without the feeling of embarrassment of having given up her first command? There were too many difficult aspects of this to make him feel remotely comfortable. He also knew her record and liked what he saw in it. She had all the makings of a superb captain.

"I'll be honest, Captain, I am not comfortable with the idea," he replied finally.

"If I thought you would be, I would never have considered this," she answered. "If you accept this, all I ask is that this be a Starfleet ship and run by Starfleet rules. Outside of that, we can work out the details and nuances as they develop."

"May I have a list of the ships needs as far as personnel?" he asked.

Kathryn handed over a second PADD. "These are the casualty lists and the positions that are now vacant," she told him. "Also included are the personnel records of the senior people in the various departments who would normally be in line to take over in this kind of situation."

Chakotay nodded. "I need a couple of hours to consider your proposal," he said finally. "I suggest that I find a place to look this over, and come up with a list of recommendations for placing my people in various slots throughout the ship. Then I can come back and we can discuss this further."

"Then you at least accept joining the two crews?" she asked.

"Yes," he informed her. "I also accept that this be a Starfleet ship. Beyond that, I need time to think."

"How about we meet here in three hours and go over it all?" she suggested. "For the moment I have the ship on course for the Alpha Quadrant and repairs are under way."

"Sounds fine," he agreed.

"Use the First Officer's office for now next to the briefing room," she suggested. "Comm me when you're ready."

The next three hours were nerve racking for both of them. Kathryn was worried that he wouldn't accept her proposal and that would make her Captain on this mission. She was confident of her abilities when in an ordinary situation, but this called for an experienced Captain if one was available. Her skills were much more in the main with science and engineering where she could use her command abilities in a more engaging capacity and be of real value to a good captain. While decent at tactics, she was out of her depth when compared to Chakotay. Voyager had been designed as a science vessel and that was why she was chosen to be it's captain and also have this as her first command. The mission from the President to apprehend Chakotay had been a complete shock, especially when she found that Tuvok would be going undercover.

Chakotay had finished his evaluation of the needs of Voyager and where his crew would best fit in within an hour. It hadn't been too difficult. Then he spent time considering whether to accept command or not. Janeway made a compelling case, he had to admit. She was also trying to accomplish the most important aspect of command and that was to look out for the welfare of her crew. She felt that he was best for that. He was tired, though. By nature a peaceful man, he had become a fierce combatant these last couple of years. Killing was not something he liked or wanted, and he felt that by taking command, he was going to be in for more of the same, albeit a bit more distant. He also wondered if he would be able to convince his crew that this would be best. He had no doubt about his command of them, but this stretched even that. In the end, though, he knew what he would have to do.

"Chakotay to Janeway," he said as he tapped the comm badge she had given him three hours before.

"_Janeway here."_

"I've finished the review and have my recommendations," he told her. He wasn't going to reveal just yet what he had decided.

_"Come to the Ready Room and we can discuss them here," _she suggested.

"I'll be right there. Chakotay out."

He had already replicated a uniform and had it on, without rank pips. He wanted to let her know he was serious about joining the crews together and that it would be a Starfleet ship. The surprised looks on the Bridge crews faces at him being in uniform was amusing, and oddly enough the small nod of approval from Tuvok was a bit comforting. He was not angry with Tuvok since the man was only doing his job when he infiltrated his cell, but he was angry at himself at having been duped. When he reached the door to the Ready Room he rang the chime and waited to be admitted. When the doors slip open, he walked in.

Kathryn was relieved when she saw him enter in uniform, though she noticed that he was not wearing any pips. At least he was taking seriously the commitments he had already made. She offered him a seat on the couch and sat beside him, taking the PADD he offered. She turned it on and read his recommendations carefully. She was not surprised that he recommended her crew members for most of the positions of authority, though he had several of his own recommended for ranks of ensign. Two stood out, though. He recommended Ayala for Tuvok's deputy in Security with the rank of Lieutenant, Junior Grade. He also recommended B'Elanna Torres for Chief Engineer with the rank full Lieutenant. He had even suggested Tom Paris as chief Helmsman with rank of Lieutenant, Junior Grade. With the exception of Torres she could see the sense in all of them, and based on her academic record, as opposed to disciplinary record, from the Academy, she could begin to see the wisdom of that recommendation, too.

"With the exception of Torres, I can see this being a good set of placements," she said when she had finished. "Do you see any trouble spots?"

Chakotay handed over a second PADD. "These are the people I would expect to cause trouble at different stages. They bear watching," he said without any hint of disappointment. In the Maquis they needed people wherever they could get them.

"I guess that leaves a big decision to make before either of us can implement any of these," she said gesturing to the first PADD. She would like to make it clear that the person who would be commanding would make the final decision, not necessarily her.

Chakotay sighed. "I accept your offer, and also accept your offer of becoming First Officer," he said very reluctantly. He saw her start to remove one of her pips and halted her with a gesture. "You won't be losing rank. I think two captains can serve on the same ship in the two positions. It's been done before quite successfully."

Kathryn grinned. "I don't think we're at the level of Kirk and Spock yet, are we?" she joked.

He smiled in return. "Not yet, but we have a long journey ahead of us, regardless of where we decide to go," he replied. He reached into his pocket and pulled out four rank pips and pinned them on himself, making his rank acceptance official.

Kathryn stood to go over to the computer to make the change of command and also turn over the command codes, but was halted by a gesture.

"Before we make this official, I want you to know I have serious reservations about assuming command over you," he let her know. "I respect why you're doing this, but I wish you hadn't felt it necessary. You're a damn good officer and from what I can see, a good Captain with a lot of potential."

Kathryn was touched. "Thank you," she replied. "I've always wondered about decisions I've made in the past, but this one I haven't had any kind of second thoughts. It's what's best for our crews, Chakotay. I think you're the best one to lead us."

"When you switch over the command codes and command, make sure that you're new command codes and security clearances match mine," he ordered. "I don't want any secrets in this command. That's not how I operate."

"Understood," she said as she made the necessary changes in the ships database and allowed Chakotay to announce his acceptance to the computer. She had a feeling it would be an interesting experience serving under this man. Her mind gave her some wicked thoughts at that double entendre, but she brushed them aside. There would be time enough for those considerations later when they got to know one another better. Besides, if he was anything like her, then protocol would probably get in the way before anything could start.

Chakotay was having similar thoughts about his new executive officer. She was beautiful and he had been mindful of that from the moment he had first seen her on his view screen. He wondered how seriously she took protocol and if she would ever consider having a relationship with someone like him. He smiled at the thought and tucked it away for further consideration later when things had gelled more between them and also the two crews. It would definitely be an interesting journey.

_**Six Years Later, Outside Starfleet Headquarters, San Francisco, Earth**_

Chakotay saw the figure sitting on the bench in the small park outside Starfleet Headquarters. The interminable debriefings were concluded and all had turned out very well. The Dominion War had ended all desire to punish or even recognize as crimes the activities of the Maquis. He had been recognized as Voyager's Captain and Commanding Officer of the last six years and understood the rationale that made that happen. He and Kathryn had spent a long time answering question, but both had been given commendations and, surprising both, promotions to Rear Admiral.

"Contemplating the universe?" he asked as he stepped up beside her and took a seat.

"A bit," she smiled at him. She looked at him in the new uniform of a Rear Admiral and had to admit, that while the black and grey were not her first choice, it looked damn good on him. "You were a lot more cautious than I would have been out there," she said what was on her mind.

He smiled. "I know," he replied. She was referring to their time on Voyager and the strategic decisions he had made, such as avoiding Borg Space. They had met up with the Borg, and became allies with Species 8472, but it had been when they were actually ready, not because of impatience or imprudence. Kathryn had not seen it that way at the time, but had accepted his decisions as she was supposed to. Not helping the telepaths to cross Devore Space had also been one where she had storngly disagreed, but he had steered clear of that region and found a wormhole that shaved off fifteen more years of their journey in the process.

"I was also wrong personally," she said after a moment or two of further thought.

Now he smiled even wider. "I know that, too," he said in a neutral tone. They had almost become lovers on New Earth, and while he had been willing to continue letting the relationship grow back on Voyager, she had not believed they should because of protocol. He had acquiesced, but had not allowed them to continue without acknowledging their commitment to one another. They had been a couple ever since, but had not taken the last step, waiting until they reached home, or the tenth year of the journey had arrived. A compromise, but a good one. Their platonic togetherness had been exclusive and neither had strayed. Love, when acknowledged, was a powerful force all its own. He had taught her that, but also had learned the full power of it himself. It had not been the right decision, but it had been a good one. Now they had four years of intimacy, in the physical sense, to make up for.

Kathryn chuckled. He was so damn self assured, but it was one of the things she loved about him. He had taught her to be a good commanding officer, and she knew now that she would have made some dreadful mistakes along the way that his experience and caution had avoided. He had also insisted that they acknowledge their love after New Earth, and while they had not been lovers, they had been exclusively together since then. During the first two years of the journey she had used some of her shore leaves to find a willing male for a bed companion for a couple of nights or so to make up for the loneliness, but Chakotay's platonic companionship had been enough the last four years. It had been rough a couple of times, she was human after all with needs and desires, but she had never gone astray. The late evening cuddling and time spent with one another had been enough.

"So what do you want to do for the next six months we have on leave?" she asked. She slipped her arm through his and leaned against him, not caring what anyone would say about the blatant PDA. They had both been given six months leave and then would be given command of the sector that the old DMZ was in and also a completely built station to have a base from that was a duplicate of the massive McKinkley Spacedock that orbited Earth. DS9 would be the main center to protect the Wormhole, but their station would be a major point of resupply, refurbishment, and first response in that region of space. Fully twenty starships would be stationed out of their Spacedock, in addition to their flagship, yet to be designated.

His smile continued. "I think that we should go off somewhere and explore what we started on New Earth, though with no parameters and protocol ideas," he suggested.

"God I was such a fool," she chuckled. She loved him, though, for the respect he gave her sense of propriety that she honestly had believed in. "How about we head to Indiana and I introduce you to my Mother, and then we take a long getaway so I can show you the real Lake George?" she asked.

He stood and offered her a hand up, kissing her as she stood. "I like that idea, Admiral Janeway," he said in a slightly husky voice.

"Admiral Janeway," she repeated. Her own smile grew. "I really like the sound of that, Admiral Chakotay. Now let's get out of here. We have some lost years to make up for."


End file.
